BIOL-L 211 : EXAM 1
137 Cards in this Set
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Why is the term nucleotide imprecise?
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It is not clear how many phosphoryl groups are attached to the nucleoside. To better specify this the nucleotide could be referred to as a nucleoside mono-, di or tri- phosphate
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Why is DNA called deoxy?
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It has only one H rather than an OH on the 2' carbon of the ribose ring
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Is the DNA double helix left or right handed?
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right handed
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What kind of bonds hold the double helix together?
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Hydrogen bonds
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There are __H bonds between G and C and ___ H bonds between A and T
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3
2
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Is the information content of DNA in the sugar phosphate backbones, the riboses, or the bases?
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only in the bases
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Primary structure relies on formation of___bonds
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peptide (covalent)
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Proteins can be both stiff and___
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flexible
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Peptide bonds are__
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stiff
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Why are peptide bonds stiff?
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Due to their partial double bond nature; there is no rotation at this bond
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Peptide bonds except proline are usually in the ___,not cis form
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trans
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For most side groups, the ___position is favored; it minimizes crowding of the two adjacent side groups
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trans
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For peptide bonds with proline, there is crowding in both the ___and ___positions so neither is favored. Often in turns
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cis, trans
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Alpha carbon bonds are __
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flexible
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One protein measurement unit is a ___and is equal to one atomic mass unit-about a hydrogen atom mass
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dalton
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Secondary structure depends on __bonds
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hydrogen
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Alpha helix
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stiff, rod-like structure that is shaped like a spring.
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Side groups determine whether or not an alpha helix is___or__
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hydrophobic or hydrophillic
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Alpha helices are stiff because the coils of the helix are stabilized by the formation of____ between Co and NH groups along the main chain.
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H bonds
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There are ___amino acids per turn of the helix
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3.6
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Two or more alpha helices can interact with each other to form_____and these are very strong and stable
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coiled-coils
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Coiled-Coils are found in proteins that must ___when pulled
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resist breakage
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Beta strands are____
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short regions of the protein in which the peptide backbone is almost fully extended
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Beta sheets are formed from a bunch of ___that are approximately parallel to each other
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Beta strands
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The Beta strands are held together by many individual ____bonds that exist at about right angles to the backbones of the Beta strands
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H
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Beta __can be either parallel or antiparallel but Beta__can have both types!!
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strands, sheets
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___interactions drive folding.
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Hydrophobic
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Van der Waals forces ___folded protein structures
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stabilize
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Domains are__
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discrete, compact regions seen in tertiary structures
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Quaternary structure only exists in proteins containing multiple ___each made of a separate peptide chain.
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subunits
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The most common types of bonds that and forces that keep subunits together are___
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H bonds, electrostatic or ionic bonds, Van der Waals forces, and hydrophobic interactions and sometimes disulfide bonds
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In electrophoresis, charged particles move in an electric field if free to move, a particle will migrate___from the same change and towards the opposite charge.
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away
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The rate of movement depends on____
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the strength of the electric field
net charge of the molecule
the amount of friction between the molecule and its environment
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The greater the strength, the ___movement
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faster
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The more charged, the __movement
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faster
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The more charged, the __movement
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faster
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The amount of friction between the molecule and its environment depends on ___
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size (number of aas)
shape (rod like vs. globular) of the molecule
viscosity of the solution it's in
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Which bonds within a peptide backbone provide it with flexibility and why?
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the bonds between the alpha carbon and both the amino nitrogen and the carbonyl carbon
they provide flexibility because they are single bonds and can rotate freely
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Which bonds within a peptide backbone provide it with stiffness and why?
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he peptide bonds between the amino nitrogens and the carbonyl carbons
because of their partial double bonds nature which inhibits rotation between these two atoms
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How many amino acids does a 44 kDa protein contain?
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400 amino acids
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What kinds of bonds stabilize alpha helical structures in proteins and between which atoms are such bonds formed?
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hyrogen bonds stabilize alpha helices and these are formed along the main backbone of the protein between CO and NH groups that are 4 amino acids apart
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Why is an alpha helix weaker in water than in oil?
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because the hydrogen bonding ability of water leads it to form such bonds with the CO and NH groups of the main backbone of alpha helices, thus disrupting the hydrogen bonding within the helix and weakening it. Oil cannot form such hydrogen bonds and thus does not weaken a helix.
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What determines whether an alpha helix is more hydrophobic or hydrophillic and why?
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the hydrophobicity or hydrophillicity of the side groups because they are on the exposed outer surface of the helix.
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Within the two dimensions of a beta sheet, what provides the covalent bonds and what provides the non-covalent bonds?
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the covalent bonds are provided by the backbones within each of the protein strands and the non covalent bonds are provided by the hydrogen bonds of CO and NH groups between the protein strands
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What force drives protein folding into its tertiary structure in aqueous environments and two forces or bonds that stabilize this structure once it is formed
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The hydrophobic effect drives protein folding and van der Waals forces and disulfide covalent bonds stabilize it
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Why don't all proteins have quaternary structure? Name 5 forces that hold such structure together
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because not all proteins contain multiple subunits.
hydrogen bonding, electrostatic interactions, van der Waals forces, hydrophobic interactions and disulfide bonds
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What does the rate of movement of a charged particle in an electric field depend on?
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strength of electric field
net charge of molecule
amount of friction between the molecule and its environment
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What are the relationships of these and the rate at which the molecule moves through the electric field?
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greater strength, faster movement
greater charge on the particle, faster the movement
lower the friction, faster the movement
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What are the three factors that affect how much friction is generated?
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size (number of aas): greater size, greater friction
shape(rod like vs. globular): globular has less friction
viscosity of the solution it is in: greater viscosity, greater friction
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What is the name of the monomer that polymerizes in order to provide the long strands used during gel electrophoresis, as well as the monomer that is used to cross link these long strands together to form a gel like substance?
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acrylamide
methylebis-acrylamide
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If you can stain a protein band in your gel and see it by eye, what's the minimum number of copies of that protein that are present in that band?
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a trillion
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List three features of covalent bonds that are important in constructing molecules such as DNA, RNA, and protein
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they are strong
they form at specific angles
they sometimes cannot rotate relative to each other
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Where are covalent bonds typically used in these molecules?
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In their backbones or main chains
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Give one example of a covalent bond that limits rotation in a protein backbone
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a peptide bond
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Name and describe the fundamental difference, at the atomic level, between the two main classes of covalent bonds
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the atoms in a polar covalent bond share electrons unequally and have a partial charge separation.
the atoms in a non polar covalent bond share electrons equally and do not have a charge separation
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Provide three examples of atom pairs that form polar covalent bonds
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C-O, O-H, and N-H
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Provide two examples of atom pairs that form non polar covalent bonds
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C-H, and C-C
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What is this equation? F=q1q2/r2D
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Coulomb's Law
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What is each term in Coulombs law mean
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F is force of attraction (or repulsion) between two particles
q1 and q2 are the charges of these two particles
r is the distance between the groups
D is the dielectric constant OF THE SOLUTION.
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What type of bond does Coulombs law apply to?
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electrostatic interactions
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How many atoms are in an H bond?
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3
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3 features of non covalent bonds ?
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are weak
can form at any angle
typically act at short distances
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When are non covalent bonds useful for building DNA, RNA and proteins?
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when the interactions need to be reversible and when atoms need to be packed closely together
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What are approximate bond energies of the covalent bonds in a solution of water and non covalent bonds in the same water solution?
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The O-H bonds of water are about 110 kcal/mol, while non covalent bonds, or hydrogen bonds, of water are about 4.5 kcal/mol
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What is special about the side group cysteine?
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two cysteines can be oxidized to form a disulfide bond and this can be broken by the re-reduction of the sulfur atoms
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What is it about prolines that make them more likely to be found in turns in the primary amino acid chain?
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It has a cyclic structure; the side group is attached to both the alpha carbon and the nitrogen of the amino group, which deforms the peptide chain
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An acid is a proton__
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donor
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a base is a proton___
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acceptor
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Which bonds along a peptide chain allow rotation?
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bond between the alpha carbon and amino nitrogen and bond between the alpha carbon and the carbonyl carbon
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Within a Beta sheet, what provides the non-covalent bonds?
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hydrogen bonds between the main chain atoms of the protein
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Proteins have quaternary structure because___
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they have more than one subunit
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During gel electrophoresis, the rate of movement of molecules depends on the ___
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net charge of the molecule and strength of the electric field
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What force is driven primarily by a resulting increase in entropy, or disorder in the the water surrounding the protein?
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hydrophobic effect
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Which level of protein structure is created primarily by this entropy increase, primary, secondary, or tertiary?
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tertiary
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For both primary and secondary levels of protein structure, name the types of bonds or forces by which they are stabilized.
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covalent bonds
hydrogen bonds
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If two cysteines were found very near each other within the primary amino acid sequence of a protein, does it suggest that the side groups from these are likely to interact with each other?
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The fact that they are near each other does not make this interaction any more likely than if they are some distance apart in the primary protein structure because when the protein folds into its final 3 dimensional structure, the folding may occur such that regions of the protein are wid…
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Why are most peptide bonds found in trans rather than in cis configuration?
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because the side groups are less likely to interfere with each other
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Which would be a stiffer structure, an alpha helix that is 40 aas long or a Beta sheet that consists of 3 antiparallel Beta strands each of which is 40 amino acids long?
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The alpha helix because it is wound very tightly and the H bonds between the atoms of the main chain run parallel to the axis of the helix which stiffens the structure even further.
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Which has a greater dipole moment, a polar covalent bond or a nonpolar covalent bond
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a polar covalent bond
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Which of the four levels of protein structure is maintained exclusively by covalent bonds?
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only primary structure
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In what direction do the H bonds form in an alpha helix? Do they form between atoms of the side groups, atoms of the main chain, or both?
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parallel to the axis of the helix
only between the atoms of the main chain
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Which bonds within the backbone of a protein provide rotational flexibility to the protein?
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the bond between the alpha carbon and the amino N and the bond between the alpha carbon and the carboxyl C
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The bonds between the alpha carbon and the amino N and between the alpha carbon and the carboxyl C are ____
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single bonds and allow rotation
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Peptide bonds are__
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partial double bonds and adopt a planar conformation and do not allow rotation
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Describe the effect of oxidizing and reducing the cysteine's environment
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oxidizing causes the disulfide bond to form, while reducing causes the disulfide bond to break
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What is the term used to quantify the extent of polarity in a polar covalent bond?
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dielectric constant or dipole moment (water is example)
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What is the name of the force that drove each subunit from its original extended conformation into its compact, three dimensional shape?
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hydrophobic effect
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How does hydrophobic effect drive protein folding?
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Water molecules are very disorded and have dipole moments. proteins typically contain some hydrophobic amion acids which cannot dissolve in water. the water molecules form cages around these amino acids, decreaseing the water's entropy or making it more ordered. as the protein randomly mo…
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What is responsible for creating Van der Waals interactions
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the weak, transient dipole moments created around each atom as a result of random and uneven movements of electrons around nucleii leads to a small level of attraction between atoms
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Where are they commonly found in proteins?
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in the interiors of water soluble proteins
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Where would an alpha helix be stiffer, in a solution of water or oil?
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in oil because H bonding by water competes with H bonding within the alpha helix
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Which type of amino acid side group holds onto its protons more tightly, one with a high Pka or a low one?
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one with a high Pka
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Does an amino acid side group that has a Pka of 10 release its proton under acidic or basic conditions?
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basic
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What is the definition of Pka?
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the PH at which half of the population of that group is protonated and half of the population of that group is not protonated
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Which, polar or nonpolar has a greater dipole moment?
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polar covalent bond
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Which is more likely to be found on the exteriors of aqueous proteins?
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polar covalent bond
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Which is more likely to be found on the interiors of aqueous proteins?
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nonpolar covalent bonds
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Is a hydrogen bond a covalent or noncovalent bond?
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noncovalent
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Name the three general features of a nucleotide
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should be deoxy at the 2' carbon, should have 3 phosphates at the 5' carbon, should have one of the four bases found in DNA
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When a peptide consisting of twenty amino acids with hydrophobic side groups is dropped into a beaker of water, what happens to the entropy of the water?
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the entropy of the water decreases because the water forms cage structures around the hydrophobic side groups, making the water more ordered
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If you watched this peptide for a while after it was dropped into the water, how would you expect its shape to change? Assume it is an extended chain when dropped
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It would become globular because the hydrophobic side groups would randomly meet and water would be excluded from between them which would make the water less ordered
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Would this be a decreased or increased state of entropy for the peptide after a while?
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decreased
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The ___the dielectric constant the better it dissolves
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higher
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Why does one solution dissolve in salt better than the other?
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solutions with high Ds weaken ionic bonds since the molecules in these solutions have greater charge separation within each molecule. Salts interact through ionic bonds and a solution with a higher D will make larger partial and neg. charges available to salt ions and make the ions less l…
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___bonds stabilize primary structures
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covalent
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_____bonds stabilize secondary structures
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hydrogen
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Why is it that most peptide bonds are in the trans, rather than the cis configuration?
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the side groups are less likely to interfere with each other
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What kinds of bonds that form along the backbone of an alpha helix of a protein give it a tremendous amount of stiffness?
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Hydrogen bonds
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If is Ph is below Pka, then is ____
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protonated
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If protonated molecule now has a charge, is on the ___
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outside
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If Ph is above Pka, is ___
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deprotonated
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Why might you think that these bonds would be weaker if the alpha helix was floating around in the cytosol compared to if it was buried in the membrane
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the water molecules present in cytosol would be making to varing degrees hydrogen bonds with the hydrogens of the amino groups in the backbone and the oxygens of the carboxyl groups in the backbone. The formation of these would come at the expense of the breakage of the hydrogen bonds bet…
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Explain what is special about the stiffness of the peptide bond that makes it different from the other covalent bonds in the backbone? What is this unique feature due to?
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It is very stiff comparatively. This is due to the partial double bond characteristic of the peptide bond due to electron sharing between the carbonyl carbon and the amino group nitrogen of the peptide bond
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In what directions do the side groups extend from amino acid found within a Beta sheet?
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perpendicular to the plane of the sheet
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What sensation does it create if all the side groups are hydrophobic?
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The sheets slide across each other with very little friction, making the substance feel very smooth
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Why does the tertiary structure change of two proteins?
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The structures will be arranged in 3D and will be arranged very differently
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Is there any difference in quaternary structures usually if there are subunits?
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NO because there is no quaternary structure to this protein. Quaternary structure is the 3D relationship of subunits to each other and this protein is not made up of subunits
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The dipole moment is ____if hydrophobic
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insignificant
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The dipole moment is ____if hydrophillic
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significant
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C-H is ____and insignificant
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hydrophobic
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N-H is ___and significant
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hydrophillic
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C-C is ____and insignificant
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hydrophobic
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O-H is ___and significant
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hydrophillic
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Hydrophobic covalent bonds
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C-H
C-C
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Hydrophilic covalent bonds
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N-H
O-H
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Which protein level structure is maintained exclusively by covalent bonds?
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Only primary
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Would an H bond be stronger in water or oil?
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Many water soluble proteins spontaneously fold into their tertiary structures, making them more ordered. This appears to violate the second law of thermodynamics which states that the spontaneous reactions must be accompanied by an increase in disorder. What occurs to let this happen with…
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Many water soluble proteins spontaneously fold into their tertiary structures, making them more ordered. This appears to violate the second law of thermodynamics which states that the spontaneous reactions must be accompanied by an increase in disorder. What occurs to let this happen with…
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Some side groups of proteins are hydrophobic and don't interact w/water. instead water forms cages around them that are very ordered strucures which decreases water's entropy. as hydrophobic regions move around randomly and begin to fold they will sometimes meet and allow the release of s…
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Lower PH=___
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acidic
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Higher PH=___
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basic
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Side groups with the highest-lowest affinity in order
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Arginine
tyrosine
lysine
cysteine
histidine
aspartic acid
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Side groups that would be completely protonated at PH 7
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arginine
tyrosine
lysine
cysteine
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Side groups that would be completely unprotonated at PH 7
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histidine
aspartic acid
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How does the Hydrophobic effect drive protein folding?
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Water molecules are very disordered and have dipole moments. Proteins typically contain some hydrophobic amino acids which cannot dissolve in water. The water molecules form cages around these amino acids, decreasing the water's entropy and making it more ordered. As the protein randomly…
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Where would an alpha helix be stiffer, in a solution of water or a solution of oil?
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in oil because the h bonding by water competes with H bonding within the alpha helix
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What chemical is added to protein samples to solve its problems ?
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SDS: sodium dodecyl sulfate
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Higher dielectric constant the ___it is to dissolve
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easier
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BIOL-L 211: DNA REPLICATION